Rearranged and tweaked until I finally have a working scikit-build setup

CMakeLists.txt

@@ -36,8 +36,6 @@ IF (NOT SKBUILD)
   MESSAGE(STATUS "Looking in ${SKBLD_DIR}/resources/cmake for CMake modules")
 ENDIF()
 
-SET(PYTHON_EXTENSION_MODULE_SUFFIX ".${Python3_SOABI}" CACHE STRING "Suffix for python extension modules")
-
 # Detect when building against a conda environment set the _using_conda variable
 # for use both in this file and in the parent
 GET_FILENAME_COMPONENT(_python_bin_dir ${Python3_EXECUTABLE} DIRECTORY)
@@ -68,7 +66,8 @@ SET(CMAKE_Fortran_MODULE_DIRECTORY ${MOD})
 
 # The source for the SWIFTEST binary and have it placed in the bin folder
 ADD_SUBDIRECTORY(${SRC} ${BIN})
-ADD_SUBDIRECTORY(${SRC}/bindings)
+
+ADD_SUBDIRECTORY(${PY})
 # # Set up test directory
 # ENABLE_TESTING()
 # ADD_SUBDIRECTORY(${TEST})

cmake/Modules/FindNETCDF.cmake

@@ -14,8 +14,7 @@ find_library(NETCDF_FORTRAN_LIBRARY NAMES netcdff HINTS ENV NETCDF_FORTRAN_HOME
 find_library(NETCDF_LIBRARY NAMES netcdf HINTS ENV NETCDF_FORTRAN_HOME ENV LD_LIBRARY_PATH)
 
 set(NETCDF_FOUND TRUE)
-set(NETCDF_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
 # Note for posterity: When building static libraries, NETCDF_FORTRAN_LIBRARY must come *before* NETCDF_LIBRARY. Otherwise you get a bunch of "undefined reference to" errors
-set(NETCDF_LIBRARIES ${NETCDF_FORTRAN_LIBRARY} ${NETCDF_LIBRARY})
+set(NETCDF_LIBRARIES ${NETCDF_FORTRAN_LIBRARY} ${NETCDF_LIBRARY} CACHE STRING "NetCDF libraries")
 
 mark_as_advanced(NETCDF_LIBRARY NETCDF_FORTRAN_LIBRARY NETCDF_INCLUDE_DIR)

setup.py

@@ -11,6 +11,8 @@
 """
 
 from skbuild import setup
+from Cython.Build import cythonize
+import os
 
 with open('version.txt') as version_file:
     version = version_file.read().strip()
@@ -43,4 +45,5 @@
             'astroquery>=0.4.6',
             'tqdm>=4.65.0',
       ],
-      packages=['swiftest'])
+      packages=['swiftest'],
+      )

src/CMakeLists.txt

@@ -136,6 +136,24 @@ ENDIF ()
 # Turn preprocessor on for all files
 SET_SOURCE_FILES_PROPERTIES(${SWIFTEST_src} ${DRIVER_src} PROPERTIES Fortran_PREPROCESS ON)
 
+
+#Set strict vs fast math flags
+STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BT)
+IF(BT STREQUAL "RELEASE" OR BT STREQUAL "PROFILE")
+   SET_PROPERTY(SOURCE ${STRICT_MATH_FILES} APPEND_STRING PROPERTY COMPILE_FLAGS "${STRICTMATH_FLAGS}")
+   SET_PROPERTY(SOURCE ${FAST_MATH_FILES} APPEND_STRING PROPERTY COMPILE_FLAGS "${FASTMATH_FLAGS}")
+ENDIF()
+
+IF(BT STREQUAL "DEBUG")
+   ADD_DEFINITIONS(-DDEBUG)
+ELSEIF(BT STREQUAL "PROFILE")
+   ADD_DEFINITIONS(-DPROFILE)
+ENDIF()
+
+#####################################################
+# Add the needed libraries and special compiler flags
+#####################################################
+
 # Create a library from the source files, except the driver
 SET(SWIFTEST_LIBRARY swiftest)
 ADD_LIBRARY(${SWIFTEST_LIBRARY} ${SWIFTEST_src})
@@ -144,10 +162,6 @@ ADD_LIBRARY(${SWIFTEST_LIBRARY} ${SWIFTEST_src})
 SET(SWIFTEST_DRIVER swiftest_driver)
 ADD_EXECUTABLE(${SWIFTEST_DRIVER} ${DRIVER_src})
 
-#####################################################
-# Add the needed libraries and special compiler flags
-#####################################################
-
 TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PUBLIC ${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS})
 
 IF(USE_OPENMP)
@@ -162,24 +176,6 @@ IF(USE_COARRAY)
     SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY LINK_FLAGS  "${Coarray_Fortran_FLAGS} ")
 ENDIF(USE_COARRAY)
 
-STRING(REPLACE ";" " " SWIFTEST_LINK_FLAGS "${CMAKE_Fortran_LINK_FLAGS} -L${LIB} ${CMAKE_LINK_LIBRARY_FLAG}${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS}")
-SET(SWIFTEST_LINK_FLAGS "${SWIFTEST_LINK_FLAGS}" CACHE STRING "Link flags to pass to setup.py")
-
-GET_TARGET_PROPERTY(SWIFTEST_INCLUDE_DIR ${SWIFTEST_DRIVER} INCLUDE_DIRECTORIES)
-SET(SWIFTEST_INCLUDE_DIR "${SWIFTEST_INCLUDE_DIR}" CACHE STRING "Include directory needed for linking the library to an executable")
-
-#Set strict vs fast math flags
-STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BT)
-IF(BT STREQUAL "RELEASE" OR BT STREQUAL "PROFILE")
-   SET_PROPERTY(SOURCE ${STRICT_MATH_FILES} APPEND_STRING PROPERTY COMPILE_FLAGS "${STRICTMATH_FLAGS}")
-   SET_PROPERTY(SOURCE ${FAST_MATH_FILES} APPEND_STRING PROPERTY COMPILE_FLAGS "${FASTMATH_FLAGS}")
-ENDIF()
-
-IF(BT STREQUAL "DEBUG")
-   ADD_DEFINITIONS(-DDEBUG)
-ELSEIF(BT STREQUAL "PROFILE")
-   ADD_DEFINITIONS(-DPROFILE)
-ENDIF()
 
 # Check to see if the compiler allows for local-spec in do concurrent statements. Set a preprocessor variable if it does
 IF (USE_OPENMP)

src/bindings/CMakeLists.txt → swiftest/CMakeLists.txt

@@ -18,22 +18,12 @@ IF(${PYTHON_VERSION_MAJOR} EQUAL 3
       ADD_COMPILE_OPTIONS("-Wno-deprecated-declarations")
 ENDIF()
 
-SET(SWIFTEST_BINDINGS swiftest_bindings)
+SET(SWIFTEST_BINDINGS _bindings)
 
-INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
-ADD_CYTHON_TARGET(${SWIFTEST_BINDINGS} bindings.pyx)
+INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR} ${MOD})
+ADD_CYTHON_TARGET(${SWIFTEST_BINDINGS})
 ADD_LIBRARY(${SWIFTEST_BINDINGS} MODULE ${SWIFTEST_BINDINGS})
-TARGET_LINK_LIBRARIES(${SWIFTEST_BINDINGS} ${SWIFTEST_LIBRARY} ${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS})
+#MESSAGE(STATUS "Module linked libraries\nswiftest: ${SWIFTEST_LIBRARY}\nnetcdf: ${NETCDF_LIBRARIES}\nLIBS: $ENV{LIBS}")
+TARGET_LINK_LIBRARIES(${SWIFTEST_BINDINGS} swiftest ${NETCDF_LIBRARIES} $ENV{LIBS})
 PYTHON_EXTENSION_MODULE(${SWIFTEST_BINDINGS})
-INSTALL(TARGETS ${SWIFTEST_BINDINGS} DESTINATION swiftest)
-
-IF(APPLE)
-   SET_TARGET_PROPERTIES(${SWIFTEST_BINDINGS} PROPERTIES INSTALL_RPATH "@loader_path")
-ELSE()
-   SET_TARGET_PROPERTIES(${SWIFTEST_BINDINGS} PROPERTIES INSTALL_RPATH "\$ORIGIN")
-ENDIF()
-
-IF(_using_conda OR DEFINED ENV{CIBUILDWHEEL})
-   MESSAGE(STATUS "Conda detected. Setting INSTALL_RPATH_USE_LINK_PATH to True")
-   SET_TARGET_PROPERTIES(${SWIFTEST_BINDINGS} PROPERTIES INSTALL_RPATH_USE_LINK_PATH True)
-ENDIF()
+INSTALL(TARGETS ${SWIFTEST_BINDINGS} LIBRARY DESTINATION swiftest)

swiftest/__init__.py

@@ -9,6 +9,6 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-from swiftest.constants import *
-from swiftest.simulation_class import Simulation
-from swiftest.swiftest_bindings import driver
+from .constants import *
+from .simulation_class import Simulation
+from ._bindings import driver